2009年10月8日 · As a member of the wwPDB, the RCSB PDB curates and annotates PDB data according to agreed upon standards. The RCSB PDB also provides a variety of tools and resources. Users can perform simple and advanced searches based on annotations relating to sequence, structure and function.

Ligand Expo (formerly Ligand Depot) provides chemical and structural information about small molecules within the structure entries of the Protein Data Bank. Tools are provided to search the PDB dictionary for chemical components, to identify structure entries containing particular small molecules, and to download the 3D structures of the small ...

Enter IDs, separated by comma or white space, to download data from the Chemical Component Dictionary (CCD) and/or Biologically Interesting Molecule Reference Dictionary (BIRD)

2024年1月8日 · Small molecules such as ions, cofactors, inhibitors, drugs, etc. are called ligands in the PDB. They are often found interacting with biological polymers (like proteins and nucleic acids) and may have structurally stabilizing or functional roles in their interactions with macromolecules. Why learn about ligands?

The Chemical Component Dictionary is as an external reference file describing all residue and small molecule components found in PDB entries. This dictionary contains detailed chemical descriptions for standard and modified amino acids/nucleotides, small molecule ligands, and solvent molecules.

These chemical descriptors uniquely define each type of ligand, based on its chemical composition and pattern of covalent bonding between atoms. This is useful for identifying all of the instances of a particular ligand in the PDB.

Dictionary of chemical components (ligands, small molecules and monomers) referred to in PDB entries and maintained by wwPDB. It provides comprehensive search facilities for finding a particular component, or determining components in structure entries or vice versa.

Search for ligands associated with PDB structures using RCSB PDB (rcsb.org), or perform component-based LigandExpo (ligand-expo.rcsb.org).

2005年1月1日 · PDB-Ligand (http://www.idrtech.com/PDB-Ligand/) is a three-dimensional structure database of small molecular ligands that are bound to larger biomolecules deposited in the Protein Data Bank (PDB). It is also a database tool that allows one to browse, classify, superimpose and visualize these structu …

BioLiP uses a composite automated and manual procedure for examining the biological relevance of ligands in the PDB database. Each entry in BioLiP contains a comprehensive list of annotations on: ligand-binding residues; ligand binding affinity …